diff --git a/.gitignore b/.gitignore
index 22dde614f696e27315f2c7d719f3a26b92be401b..01306d4cd381e506cf397a21ad90858f0266c453 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,3 +3,4 @@
.RData
.Ruserdata
packrat/lib*/
+inst/doc
diff --git a/examples/square_1x1_quad8_1e2.vtu b/examples/square_1x1_quad8_1e2.vtu
deleted file mode 100644
index 32a0c26bd0dc9a87fa9d9075370f82e41e0058a3..0000000000000000000000000000000000000000
--- a/examples/square_1x1_quad8_1e2.vtu
+++ /dev/null
@@ -1,33 +0,0 @@
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diff --git a/examples/test_r2ogs6.R b/examples/test_r2ogs6.R
deleted file mode 100644
index 708d034101a167ca3bb464809de6a9f7baa39474..0000000000000000000000000000000000000000
--- a/examples/test_r2ogs6.R
+++ /dev/null
@@ -1,234 +0,0 @@
-detach("package:r2ogs6", unload=TRUE)
-library(r2ogs6)
-
-
-#This is where the user defines their data.
-
-#============================== SET UP SIMULATION OBJECT ================================
-
-#If you want to test this, don't forget to alter the paths to fit your system!
-
-#First, we need to create a simulation object.
-
-ogs6_obj <- OGS6$new(sim_name = "my_sim",
- sim_id = 1,
- sim_path = "D:\\OGS_Sim\\",
- ogs_bin_path = "D:\\Programme\\OpenGeoSys\\ogs-6.3.2-Windows-10.0.14393-x64-python-3.7.2-de-utils\\bin\\")
-
-
-#============================== ADD .gml DATA ================================
-
-#(source: HydroComponent Benchmarks -> IdealGas -> flow_no_strain -> square_1x1.gml)
-
-#Add some geometry
-input_add(r2ogs6_gml(name = "square_1x1_geometry",
- points = tibble::tibble(x = c(0, 0, 1, 1),
- y = c(0, 1, 0, 1),
- z = c(0, 0, 0, 0),
- name = c("origin", rep("", 3))),
- polylines = list(list(name = "left", c(0, 1)),
- list(name = "right", c(2, 3)),
- list(name = "bottom", c(0, 2)),
- list(name = "top", c(1, 3)))),
- ogs6_obj)
-
-#============================== ADD .vtu DATA ================================
-
-#Let's add our data for the .vtk file, which contains information about our mesh.
-
-# #This calls an external script (which is why we needed to specify some paths earlier)
-# generate_structured_mesh(ogs6_obj, "-e quad --lx 1 --ly 1 --lz 1")
-
-#To make sure our geometry is right, let's copy the .vtu from the benchmark
-# we're trying to reverse engineer...
-
-pick_file(ogs6_obj)
-
-
-#============================== ADD .prj DATA ================================
-
-#Let's add our data for the .prj file, arguably the most important file.
-#(source: HydroComponent Benchmarks -> IdealGas -> flow_no_strain -> flow_no_strain.prj)
-
-#We need:
-#1. Either one mesh and one geometry file OR multiple mesh files (for the latter case: Skip to
-# previous part and call generate_structured_mesh at least one more time)
-
-#2. One or more process elements:
-input_add(r2ogs6_process(name = "HM",
- type = "HYDRO_MECHANICS",
- integration_order = 3,
- dimension = 2,
- constitutive_relation = c(type = "LinearElasticIsotropic",
- youngs_modulus = "E",
- poissons_ratio = "nu"),
- process_variables = c(displacement = "displacement",
- pressure = "pressure"),
- secondary_variables = list(c("sigma_xx", "sigma_xx"),
- c("sigma_yy", "sigma_yy"),
- c("sigma_zz", "sigma_zz"),
- c("sigma_xy", "sigma_xy"),
- c("epsilon_xx", "epsilon_xx"),
- c("epsilon_yy", "epsilon_yy"),
- c("epsilon_zz", "epsilon_zz"),
- c("epsilon_xy", "epsilon_xy"),
- c("velocity", "velocity")),
- specific_body_force = c(0, 0)),
- ogs6_obj)
-
-#3. One time_loop element:
-input_add(r2ogs6_time_loop(processes = list(r2ogs6_tl_process(ref = "HM",
- nonlinear_solver = "basic_newton",
- convergence_criterion = list(type = "PerComponentDeltaX",
- norm_type = "NORM2",
- reltols = "5e-8 1e10 1e10"),
- time_discretization = list(type = "BackwardEuler"),
- time_stepping = list(type = "FixedTimeStepping",
- t_initial = 0,
- t_end = 100,
- timesteps = list(pair = list(rep = 1,
- delta_t = 0.1))
- )
- )),
- output = r2ogs6_tl_output(type = "VTK",
- prefix = "flow_no_strain_pcs_{:process_id}",
- suffix = "_ts_{:timestep}_t_{:time}",
- timesteps = list(pair = list(rep = 1,
- each_steps = 1000)),
- variables = list("displacement",
- "pressure",
- "sigma_xx",
- "sigma_yy",
- "sigma_zz",
- "sigma_xy",
- "epsilon_xx",
- "epsilon_yy",
- "epsilon_zz",
- "epsilon_xy",
- "velocity"))),
- ogs6_obj)
-
-#4. One or more medium elements:
-input_add(r2ogs6_medium(phases = list(r2ogs6_medium_phase(type = "Gas",
- properties = list(r2ogs6_medium_property(name = "viscosity",
- type = "Constant",
- value = 1e-5),
- r2ogs6_medium_property(name = "density",
- type = "IdealGasLaw"),
- r2ogs6_medium_property(name = "molar_mass",
- type = "Constant",
- value = 0.028964397787206768))),
- r2ogs6_medium_phase(type = "Solid",
- properties = list(r2ogs6_medium_property(name = "porosity",
- type = "Constant",
- value = 0.03),
- r2ogs6_medium_property(name = "density",
- type = "Constant",
- value = 2.17e3),
- r2ogs6_medium_property(name = "biot_coefficient",
- type = "Constant",
- value = 0.6)))),
- properties = list(r2ogs6_medium_property(name = "reference_temperature",
- type = "Constant",
- value = 293.15),
- r2ogs6_medium_property(name = "permeability",
- type = "Constant",
- value = 1e-4))),
- ogs6_obj)
-
-#5. One or more parameters:
-input_add(r2ogs6_parameter(name = "E",
- type = "Constant",
- values = 1e9),
- ogs6_obj)
-
-input_add(r2ogs6_parameter(name = "nu",
- type = "Constant",
- values = .3),
- ogs6_obj)
-
-input_add(r2ogs6_parameter(name = "displacement0",
- type = "Constant",
- values = c(0, 0)),
- ogs6_obj)
-
-input_add(r2ogs6_parameter(name = "pressure0",
- type = "Constant",
- values = 1e5),
- ogs6_obj)
-
-input_add(r2ogs6_parameter(name = "zero",
- type = "Constant",
- values = 0),
- ogs6_obj)
-
-input_add(r2ogs6_parameter(name = "flux",
- type = "Constant",
- values = 1e-3),
- ogs6_obj)
-
-
-#6. One or more process variables
-input_add(r2ogs6_process_variable(name = "displacement",
- components = 2,
- order = 2,
- initial_condition = "displacement0",
- boundary_conditions = list(r2ogs6_boundary_condition(type = "Dirichlet",
- parameter = "zero",
- component = 0,
- geometrical_set = "square_1x1_geometry",
- geometry = "left"),
- r2ogs6_boundary_condition(type = "Dirichlet",
- parameter = "zero",
- component = 1,
- geometrical_set = "square_1x1_geometry",
- geometry = "bottom"),
- r2ogs6_boundary_condition(type = "Dirichlet",
- parameter = "zero",
- component = 0,
- geometrical_set = "square_1x1_geometry",
- geometry = "right"),
- r2ogs6_boundary_condition(type = "Dirichlet",
- parameter = "zero",
- component = 1,
- geometrical_set = "square_1x1_geometry",
- geometry = "top"))),
- ogs6_obj)
-
-input_add(r2ogs6_process_variable(name = "pressure",
- components = 1,
- order = 1,
- initial_condition = "pressure0",
- boundary_conditions = list(r2ogs6_boundary_condition(type = "Neumann",
- parameter = "flux",
- component = 0,
- geometrical_set = "square_1x1_geometry",
- geometry = "left")
- )
- ),
- ogs6_obj)
-
-#7. One or more nonlinear solvers
-input_add(r2ogs6_nonlinear_solver(name = "basic_newton",
- type = "Newton",
- max_iter = 50,
- linear_solver = "general_linear_solver"),
- ogs6_obj)
-
-#8. One or more linear solvers
-input_add(r2ogs6_linear_solver(name = "general_linear_solver",
- eigen = list(solver_type = "BiCGSTAB",
- precon_type = "ILUT",
- max_iteration_step = 10000,
- error_tolerance = 1e-16),
- lis = "-i bicgstab -p ilu -tol 1e-16 -maxiter 10000"),
- ogs6_obj)
-
-
-#OPTIONAL: A test definition
-
-#============================== Execution ================================
-
-#Calls ogs6 object validator functions, exports all necessary files and starts OpenGeoSys6
-
-run_simulation(ogs6_obj)